ABSTRACT
MICAL proteins represent a unique family of actin regulators crucial for synapse development, membrane trafficking, and cytokinesis. Unlike classical actin regulators, MICALs catalyze the oxidation of specific residues within actin filaments to induce robust filament disassembly. The potent activity of MICALs requires tight control to prevent extensive damage to actin cytoskeleton. However, the molecular mechanism governing MICALs' activity regulation remains elusive. Here, we report the cryo-EM structure of MICAL1 in the autoinhibited state, unveiling a head-to-tail interaction that allosterically blocks enzymatic activity. The structure also reveals the assembly of C-terminal domains via a tripartite interdomain interaction, stabilizing the inhibitory conformation of the RBD. Our structural, biochemical, and cellular analyses elucidate a multi-step mechanism to relieve MICAL1 autoinhibition in response to the dual-binding of two Rab effectors, revealing its intricate activity regulation mechanisms. Furthermore, our mutagenesis study of MICAL3 suggests the conserved autoinhibition and relief mechanisms among MICALs.
Subject(s)
Actins , Cryoelectron Microscopy , Mixed Function Oxygenases , Humans , Actins/metabolism , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Microfilament Proteins/metabolism , Microfilament Proteins/genetics , Microfilament Proteins/chemistry , Protein Binding , Actin Cytoskeleton/metabolism , Models, Molecular , rab GTP-Binding Proteins/metabolism , rab GTP-Binding Proteins/genetics , Cytoskeletal Proteins/metabolism , Cytoskeletal Proteins/chemistry , Cytoskeletal Proteins/genetics , Protein Domains , CalponinsABSTRACT
Flavin-containing monooxygenase from Methylophaga sp. (mFMO) was previously discovered to be a valuable biocatalyst used to convert small amines, such as trimethylamine, and various indoles. As FMOs are also known to act on sulfides, we explored mFMO and some mutants thereof for their ability to convert prochiral aromatic sulfides. We included a newly identified thermostable FMO obtained from the bacterium Nitrincola lacisaponensis (NiFMO). The FMOs were found to be active with most tested sulfides, forming chiral sulfoxides with moderate-to-high enantioselectivity. Each enzyme variant exhibited a different enantioselective behavior. This shows that small changes in the substrate binding pocket of mFMO influence selectivity, representing a tunable biocatalyst for enantioselective sulfoxidations.
Subject(s)
Oxygenases , Oxygenases/metabolism , Oxygenases/chemistry , Substrate Specificity , Biocatalysis , Oxidation-Reduction , Sulfides/metabolism , Sulfides/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Sulfoxides/chemistry , Sulfoxides/metabolism , Catalysis , Flavins/metabolism , Flavins/chemistry , Stereoisomerism , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Mixed Function Oxygenases/geneticsABSTRACT
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes which are categorized in the CAZy database under auxiliary activities families AA9-11, 13, 14-17. Secreted by various microorganisms, they play a crucial role in carbon recycling, particularly in fungal saprotrophs. LPMOs oxidize polysaccharides through monooxygenase/peroxygenase activities and exhibit peroxidase and oxidase activities, with variations among different families. AA16, a newly identified LPMO family, is noteworthy due to limited studies on its members, thus rendering the characterization of AA16 enzymes vital for addressing controversies around their functions. This study focused on heterologous expression and biochemical study of an AA16 LPMO from Thermothelomyces thermophilus (formerly known as Myceliophthora thermophila), namely MtLPMO16A. Substrate specificity evaluation of MtLPMO16A showed oxidative cleavage of hemicellulosic substrates and no activity on cellulose, accompanied by a strong oxidase activity. A comparative analysis with an LPMO from AA9 family explored correlations between these families, while MtLPMO16A was shown to boost the activity of some AA9 family LPMOs. The results offer new insights into the AA16 family's action mode and microbial hemicellulose decomposition mechanisms in nature.
Subject(s)
Mixed Function Oxygenases , Polysaccharides , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Mixed Function Oxygenases/genetics , Polysaccharides/chemistry , Polysaccharides/metabolism , Substrate Specificity , Fungal Proteins/metabolism , Fungal Proteins/chemistry , Fungal Proteins/genetics , Sordariales/enzymologyABSTRACT
The unspecific peroxygenase (UPO) from Agrocybe aegerita (rAaeUPO-PaDa-I-H) is an effective and practical biocatalyst for the oxidative expansion of furfuryl alcohols/amines on a preparative scale, using the Achmatowicz and aza-Achmatowicz reaction. The high activity and stability of the enzyme, which can be produced on a large scale as an air-stable lyophilised powder, renders it a versatile and scalable biocatalyst for the preparation of synthetically valuable 6-hydroxypyranones and dihydropiperidinones. In several cases, the biotransformation out-performed the analogous chemo-catalysed process, and operates under milder and greener reaction conditions.
Subject(s)
Agrocybe , Mixed Function Oxygenases , Agrocybe/enzymology , Amines/chemistry , Amines/metabolism , Biocatalysis , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Molecular StructureABSTRACT
A novel optical lactate biosensor is presented that utilizes a colorimetric interaction between H2O2 liberated by a binary enzymatic reaction and bis(neocuproine)copper(II) complex ([Cu(Nc)2]2+) known as CUPRAC (cupric reducing antioxidant capacity) reagent. In the first step, lactate oxidase (LOx) and pyruvate oxidase (POx) were separately immobilized on silanized magnetite nanoparticles (SiO2@Fe3O4 NPs), and thus, 2 mol of H2O2 was released per 1 mol of the substrate due to a sequential enzymatic reaction of the mixture of LOx-SiO2@Fe3O4 and POx-SiO2@Fe3O4 NPs with lactate and pyruvate, respectively. In the second step, the absorbance at 450 nm of the yellow-orange [Cu(Nc)2]+ complex formed through the color reaction of enzymatically produced H2O2 with [Cu(Nc)2]2+ was recorded. The results indicate that the developed colorimetric binary enzymatic biosensor exhibits a broad linear range of response between 0.5 and 50.0 µM for lactate under optimal conditions with a detection limit of 0.17 µM. The fabricated biosensor did not respond to other saccharides, while the positive interferences of certain reducing compounds such as dopamine, ascorbic acid, and uric acid were minimized through their oxidative removal with a pre-oxidant (NaBiO3) before enzymatic and colorimetric reactions. The fabricated optical biosensor was applied to various samples such as artificial blood, artificial/real sweat, and cow milk. The high recovery values (close to 100%) achieved for lactate-spiked samples indicate an acceptable accuracy of this colorimetric biosensor in the determination of lactate in real samples. Due to the increase in H2O2 production with the bienzymatic lactate sensor, the proposed method displays double-fold sensitivity relative to monoenzymatic biosensors and involves a neat color reaction with cupric-neocuproine having a clear stoichiometry as opposed to the rather indefinite stoichiometry of analogous redox dye methods.
Subject(s)
Biosensing Techniques , Colorimetry , Copper , Enzymes, Immobilized , Hydrogen Peroxide , Lactic Acid , Magnetite Nanoparticles , Mixed Function Oxygenases , Pyruvate Oxidase , Biosensing Techniques/methods , Colorimetry/methods , Enzymes, Immobilized/chemistry , Enzymes, Immobilized/metabolism , Mixed Function Oxygenases/chemistry , Mixed Function Oxygenases/metabolism , Copper/chemistry , Magnetite Nanoparticles/chemistry , Pyruvate Oxidase/chemistry , Pyruvate Oxidase/metabolism , Lactic Acid/analysis , Lactic Acid/chemistry , Hydrogen Peroxide/chemistry , Limit of Detection , Animals , Silicon Dioxide/chemistry , PhenanthrolinesABSTRACT
Enzymatic oxygenation of various cyclic ketones into lactones via Baeyer-Villiger monooxygenases (BVMOs) could provide a promising route for synthesizing fragrances and pharmaceutical ingredients. However, unsatisfactory catalytic activity and thermostability restricted their applications in the pharmaceutical and food industries. In this study, we successfully improved the catalytic activity and thermostability of a Baeyer-Villiger monooxygenase (OgBVMO) from Oceanicola granulosus by reshaping the binding pocket. As a result, mutant OgBVMO-Re displayed a 1.0- to 6.4-fold increase in the activity toward branched cyclic ketones tested, accompanied by a 3 °C higher melting point, and a 2-fold longer half-life time (t1/2 (45 °C)). Molecular dynamics simulations revealed that reshaping the binding pocket achieved strengthened motion correlation between amino acid residues, appropriate size of the substrate-binding pocket, beneficial surface characteristics, lower energy barriers, and shorter nucleophilic distance. This study well demonstrated the trade-off between the enzyme activity and thermostability by reshaping the substrate-binding pocket, paving the way for further engineering other enzymes.
Subject(s)
Enzyme Stability , Mixed Function Oxygenases , Mixed Function Oxygenases/chemistry , Mixed Function Oxygenases/genetics , Mixed Function Oxygenases/metabolism , Binding Sites , Kinetics , Biocatalysis , Fungal Proteins/chemistry , Fungal Proteins/genetics , Fungal Proteins/metabolism , Substrate Specificity , Molecular Dynamics Simulation , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Hot Temperature , Ketones/chemistry , Ketones/metabolismABSTRACT
Lytic polysaccharide monooxygenase (LPMO)-catalyzed oxidative processes play a major role in natural biomass conversion. Despite their oxidative cleavage at the surface of polysaccharides, understanding of their mode of action, and the impact of structural patterns of the cellulose fiber on LPMO activity is still not fully understood. In this work, we investigated the action of two different LPMOs from Podospora anserina on celluloses showing different structural patterns. For this purpose, we prepared cellulose II and cellulose III allomorphs from cellulose I cotton linters, as well as amorphous cellulose. LPMO action was monitored in terms of surface morphology, molar mass changes and monosaccharide profile. Both PaLPMO9E and PaLPMO9H were active on the different cellulose allomorphs (I, II and III), and on amorphous cellulose (PASC) whereas they displayed a different behavior, with a higher molar mass decrease observed for cellulose I. Overall, the pretreatment with LPMO enzymes clearly increased the accessibility of all types of cellulose, which was quantified by the higher carboxylate content after carboxymethylation reaction on LPMO-pretreated celluloses. This work gives more insight into the action of LPMOs as a tool for deconstructing lignocellulosic biomass to obtain new bio-based building blocks.
Subject(s)
Cellulose , Mixed Function Oxygenases , Cellulose/chemistry , Cellulose/metabolism , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Podospora/enzymology , Polysaccharides/chemistry , Polysaccharides/metabolism , BiomassABSTRACT
The synthesis of steroids is challenging through multistep steroidal core modifications with high site-selectivity and productivity. In this work, a novel enzymatic cascade system was constructed for synthesis of testolactone by specific C17 lactonization/Δ1-dehydrogenation from inexpensive androstenedione using an engineered polycyclic ketone monooxygenase (PockeMO) and an appropriate 3-ketosteroid-Δ1-dehydrogenase (ReKstD). The focused saturation mutagenesis in the substrate binding pocket was implemented for evolution of PockeMO to eliminate the bottleneck effect. A best mutant MU3 (I225L/L226V/L532Y) was obtained with 20-fold higher specific activity compared to PockeMO. The catalytic efficiency (kcat/Km) of MU3 was 171-fold higher and the substrate scope shifted to polycyclic ketones. Molecular dynamic simulations suggested that the activity was improved by stabilization of the pre-lactonization state and generation of productive orientation of 4-AD mediated by distal L532Y mutation. Based on that, the three genes, MU3, ReKstD and a ketoreductase for NADPH regeneration, were rationally integrated in one cell via expression fine-tuning to form the efficient single cell catalyst E. coli S9. The single whole-cell biocatalytic process was scaled up and could generate 9.0 g/L testolactone with the high space time yield of 1 g/L/h without steroidal by-product, indicating the potential for site-specific and one-pot synthesis of steroid.
Subject(s)
Mixed Function Oxygenases , Mixed Function Oxygenases/genetics , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Escherichia coli/genetics , Ketones/chemistry , Ketones/metabolism , Protein Engineering/methods , Substrate Specificity , Molecular Dynamics Simulation , KineticsABSTRACT
Baeyer-Villiger monooxygenases (BVMOs) play crucial roles in the core-structure modification of natural products. They catalyze lactone formation by selective oxygen insertion into a carbon-carbon bond adjacent to a carbonyl group (Baeyer-Villiger oxidation, BVO). The homologous bacterial BVMOs, BraC and PxaB, thereby process bicyclic dihydroindolizinone substrates originating from a bimodular nonribosomal peptide synthetase (BraB or PxaA). While both enzymes initially catalyze the formation of oxazepine-dione intermediates following the identical mechanism, the final natural product spectrum diverges. For the pathway involving BraC, the exclusive formation of lipocyclocarbamates, the brabantamides, was reported. The pathway utilizing PxaB solely produces pyrrolizidine alkaloids, the pyrrolizixenamides. Surprisingly, replacing pxaB within the pyrrolizixenamide biosynthetic pathway by braC does not change the product spectrum to brabantamides. Factors controlling this product selectivity have remained elusive. In this study, we set out to solve this puzzle by combining the total synthesis of crucial pathway intermediates and anticipated products with in-depth functional in vitro studies on both recombinant BVMOs. This work shows that the joint oxazepine-dione intermediate initially formed by both BVMOs leads to pyrrolizixenamides upon nonenzymatic hydrolysis, decarboxylative ring contraction, and dehydration. Brabantamide biosynthesis is enzyme-controlled, with BraC efficiently transforming all the accepted substrates into its cognate final product scaffold. PxaB, in contrast, shows only considerable activity toward brabantamide formation for the substrate analog with a natural brabantamide-type side chain structure, revealing substrate-controlled product selectivity.
Subject(s)
Mixed Function Oxygenases , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Alkaloids/chemistry , Alkaloids/metabolism , Biocatalysis , Molecular Structure , Substrate SpecificityABSTRACT
In this paper, a novel fluorescent detection method for glucose and lactic acid was developed based on fluorescent iron nanoclusters (Fe NCs). The Fe NCs prepared using hemin as the main raw material exhibited excellent water solubility, bright red fluorescence, and super sensitive response to hydrogen peroxide (H2O2). This paper demonstrates that Fe NCs exhibit excellent peroxide-like activity, catalyzing H2O2 to produce hydroxyl radicals (â¢OH) that can quench the red fluorescence of Fe NCs. In this paper, a new type of glucose sensor was established by combining Fe NCs with glucose oxidase (GluOx). With the increase in glucose content, the fluorescence of Fe NCs decreases correspondingly, and the glucose content can be detected in the scope of 0-200 µmol·L-1 (µM). Similarly, the lactic acid sensor can also be established by combining Fe NCs with lactate oxidase (LacOx). With the increase in lactic acid concentration, the fluorescence of Fe NCs decreases correspondingly, and the lactic acid content can be detected in the range of 0-100 µM. Furthermore, Fe NCs were used in the preparation of gel test strip, which can be used to detect H2O2, glucose and lactic acid successfully by the changes of fluorescent intensity.
Subject(s)
Glucose Oxidase , Glucose , Hydrogen Peroxide , Iron , Lactic Acid , Lactic Acid/analysis , Lactic Acid/chemistry , Glucose/analysis , Glucose/chemistry , Hydrogen Peroxide/chemistry , Hydrogen Peroxide/analysis , Iron/chemistry , Glucose Oxidase/chemistry , Glucose Oxidase/metabolism , Biosensing Techniques/methods , Fluorescence , Spectrometry, Fluorescence/methods , Fluorescent Dyes/chemistry , Mixed Function Oxygenases/chemistry , Mixed Function Oxygenases/metabolism , Metal Nanoparticles/chemistryABSTRACT
Background: White-rot fungi and bacteria communities are unique ecosystems with different types of symbiotic interactions occurring during wood decomposition, such as cooperation, mutualism, nutritional competition, and antagonism. The role of chitin-active lytic polysaccharide monooxygenases (LPMOs) in these symbiotic interactions is the subject of this study. Method: In this study, bioinformatics tools were used to analyze the sequence and structure of putative LPMOs mined by hidden Markov model (HMM) profiles from the bacterial metagenomic DNA database of collected humus samples around white-rot fungi in Cuc Phuong primary forest, Vietnam. Two genes encoding putative LPMOs were expressed in E. coli and purified for enzyme activity assay. Result: Thirty-one full-length proteins annotated as putative LPMOs according to HMM profiles were confirmed by amino acid sequence comparison. The comparison results showed that although the amino acid sequences of the proteins were very different, they shared nine conserved amino acids, including two histidine and one phenylalanine that characterize the H1-Hx-Yz motif of the active site of bacterial LPMOs. Structural analysis of these proteins revealed that they are multidomain proteins with different functions. Prediction of the catalytic domain 3-D structure of these putative LPMOs using Alphafold2 showed that their spatial structures were very similar in shape, although their protein sequences were very different. The results of testing the activity of proteins GL0247266 and GL0183513 show that they are chitin-active LPMOs. Prediction of the 3-D structures of these two LPMOs using Alphafold2 showed that GL0247266 had five functional domains, while GL0183513 had four functional domains, two of which that were similar to the GbpA_2 and GbpA_3 domains of protein GbpA of Vibrio cholerae bacteria. The GbpA_2 - GbpA_3 complex was also detected in 11 other proteins. Based on the structural characteristics of functional domains, it is possible to hypothesize the role of chitin-active GbpA-like LPMOs in the relationship between fungal and bacterial communities coexisting on decomposing trees in primary forests.
Subject(s)
Mixed Function Oxygenases , Vietnam , Mixed Function Oxygenases/genetics , Mixed Function Oxygenases/chemistry , Mixed Function Oxygenases/metabolism , Forests , Chitin/metabolism , Metagenomics , Metagenome , Amino Acid SequenceABSTRACT
The high level of lactate in tumor microenvironment not only promotes tumor development and metastasis, but also induces immune escape, which often leads to failures of various tumor therapy strategies. We here report a sono-triggered cascade lactate depletion strategy by using semiconducting polymer nanoreactors (SPNLCu) for cancer cuproptosis-immunotherapy. The SPNLCu mainly contain a semiconducting polymer as sonosensitizer, lactate oxidase (LOx) conjugated via a reactive oxygen species (ROS)-cleavable linker and chelated Cu2+. Upon ultrasound (US) irradiation, the semiconducting polymer generates singlet oxygen (1O2) to cut ROS-cleavable linker to allow the release of LOx that catalyzes lactate depletion to produce hydrogen peroxide (H2O2). The Cu2+ will be reduced to Cu+ in tumor microenvironment, which reacts with the produced H2O2 to obtain hydroxyl radical (â OH) that further improves LOx release via destroying ROS-cleavable linkers. As such, sono-triggered cascade release of LOx achieves effective lactate depletion, thus relieving immunosuppressive roles of lactate. Moreover, the toxic Cu+ induces cuproptosis to cause immunogenic cell death (ICD) for activating antitumor immunological effect. SPNLCu are used to treat both subcutaneous and deep-tissue orthotopic pancreatic cancer with observably enhanced efficacy in restricting the tumor growths. This study thus provides a precise and effective lactate depletion tactic for cancer therapy.
Subject(s)
Copper , Immunotherapy , Lactic Acid , Pancreatic Neoplasms , Polymers , Pancreatic Neoplasms/metabolism , Pancreatic Neoplasms/pathology , Pancreatic Neoplasms/drug therapy , Pancreatic Neoplasms/therapy , Lactic Acid/chemistry , Lactic Acid/metabolism , Polymers/chemistry , Polymers/pharmacology , Copper/chemistry , Humans , Animals , Mice , Semiconductors , Reactive Oxygen Species/metabolism , Hydrogen Peroxide/metabolism , Hydrogen Peroxide/chemistry , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Ultrasonic Waves , Cell Line, Tumor , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacologyABSTRACT
Intrinsic characteristics of microorganisms, including non-specific metabolism sites, toxic byproducts, and uncontrolled proliferation constrain their exploitation in medical applications such as tumor therapy. Here, the authors report an engineered biohybrid that can efficiently target cancerous sites through a pre-determined metabolic pathway to enable precise tumor ablation. In this system, DH5α Escherichia coli is engineered by the introduction of hypoxia-inducible promoters and lactate oxidase genes, and further surface-armored with iron-doped ZIF-8 nanoparticles. This bioengineered E. coli can produce and secrete lactate oxidase to reduce lactate concentration in response to hypoxic tumor microenvironment, as well as triggering immune activation. The peroxidase-like functionality of the nanoparticles extends the end product of the lactate metabolism, enabling the conversion of hydrogen peroxide (H2O2) into highly cytotoxic hydroxyl radicals. This, coupled with the transformation of tirapazamine loaded on nanoparticles to toxic benzotriazinyl, culminates in severe tumor cell ferroptosis. Intravenous injection of this biohybrid significantly inhibits tumor growth and metastasis.
Subject(s)
Escherichia coli , Ferroptosis , Mixed Function Oxygenases , Tumor Microenvironment , Tumor Microenvironment/drug effects , Animals , Ferroptosis/drug effects , Mice , Escherichia coli/metabolism , Cell Line, Tumor , Humans , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Tirapazamine/chemistry , Tirapazamine/pharmacology , Hydrogen Peroxide/metabolism , Hydrogen Peroxide/chemistry , Metal-Organic Frameworks/chemistry , Imidazoles/chemistry , Lactic Acid/chemistry , Nanoparticles/chemistry , Hydroxyl Radical/metabolism , Hydroxyl Radical/chemistry , Neoplasms/drug therapy , Neoplasms/pathology , Neoplasms/metabolism , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacologyABSTRACT
CreE is a flavin-dependent monooxygenase (FMO) that catalyzes three sequential nitrogen oxidation reactions of L-aspartate to produce nitrosuccinate, contributing to the biosynthesis of the antimicrobial and antiproliferative nautral product, cremeomycin. This compound contains a highly reactive diazo functional group for which the reaction of CreE is essential to its formation. Nitro and diazo functional groups can serve as potent electrophiles, important in some challenging nucleophilic addition reactions. Formation of these reactive groups positions CreE as a promising candidate for biomedical and synthetic applications. Here, we present the catalytic mechanism of CreE and the identification of active site residues critical to binding L-aspartate, aiding in future enzyme engineering efforts. Steady-state analysis demonstrated that CreE is very specific for NADPH over NADH and performs a highly coupled reaction with L-aspartate. Analysis of the rapid-reaction kinetics showed that flavin reduction is very fast, along with the formation of the oxygenating species, the C4a-hydroperoxyflavin. The slowest step observed was the dehydration of the flavin. Structural analysis and site-directed mutagenesis implicated T65, R291, and R440 in the binding L-aspartate. The data presented describes the catalytic mechanism and the active site architecture of this unique FMO.
Subject(s)
Aspartic Acid , Catalytic Domain , Mixed Function Oxygenases , Kinetics , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Mixed Function Oxygenases/genetics , Aspartic Acid/chemistry , Aspartic Acid/metabolism , Biocatalysis , Oxidation-Reduction , NADP/metabolism , NADP/chemistry , Mutagenesis, Site-DirectedABSTRACT
Baeyer-Villiger monooxygenases belong to a family of flavin-binding proteins that catalyze the Baeyer-Villiger (BV) oxidation of ketones to produce lactones or esters, which are important intermediates in pharmaceuticals or sustainable materials. Phenylacetone monooxygenase (PAMO) from Thermobifida fusca with moderate thermostability catalyzes the oxidation of aryl ketone substrates, but is limited by high specificity and narrow substrate scope. In the present study, we applied loop optimization by loop swapping followed by focused saturation mutagenesis in order to evolve PAMO mutants capable of catalyzing the regioselective BV oxidation of cyclohexanone and cyclobutanone derivatives with formation of either normal or abnormal esters or lactones. We further modulated PAMO to increase enantioselectivity. Crystal structure studies indicate that rotation occurs in the NADP-binding domain and that the high B-factor region is predominantly distributed in the catalytic pocket residues. Computational analyses further revealed dynamic character in the catalytic pocket and reshaped hydrogen bond interaction networks, which is more favorable for substrate binding. Our study provides useful insights for studying enzyme-substrate adaptations.
Subject(s)
Mixed Function Oxygenases , Protein Engineering , Thermobifida , Stereoisomerism , Substrate Specificity , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Mixed Function Oxygenases/genetics , Thermobifida/enzymology , Thermobifida/metabolism , Oxidation-Reduction , Biocatalysis , Catalytic Domain , Models, MolecularABSTRACT
Indole monooxygenases (IMOs) are enzymes from the family of Group E monooxygenases, requiring flavin adenine dinucleotide (FAD) for their activities. IMOs play important roles in both sulfoxidation and epoxidation reactions. The broad substrate range and high selectivity of IMOs make them promising biocatalytic tools for synthesizing chiral compounds. In the present study, quantum chemical calculations using the cluster approach were performed to investigate the reaction mechanism and the enantioselectivity of the IMO from Variovorax paradoxus EPS (VpIndA1). The sulfoxidation of methyl phenyl sulfide (MPS) and the epoxidation of indene were chosen as the representative reactions. The calculations confirmed that the FADOOH intermediate is the catalytic species in the VpIndA1 reactions. The oxidation of MPS adopts a one-step mechanism involving the direct oxygen-transfer from FADOOH to the substrate and the proton transfer from the -OH group back to FAD, while the oxidation of indene follows a stepwise mechanism involving a carbocation intermediate. It was computationally predicted that VpIndA1 prefers the formation of (S)-product for the MPS sulfoxidation and (1S,2R)-product for the indene epoxidation, consistent with the experimental observations. Importantly, the factors controlling the stereo-preference of the two reactions are identified. The findings in the present study provide valuable insights into the VpIndA1-catalyzed reactions, which are essential for the rational design of this enzyme and other IMOs for industrial applications. It is also worth emphasizing that the quantum chemical cluster approach is again demonstrated to be powerful in studying the enantioselectivity of enzymatic reactions.
Subject(s)
Mixed Function Oxygenases , Oxidation-Reduction , Stereoisomerism , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Quantum Theory , Sulfides/chemistry , Sulfides/metabolism , Indoles/chemistry , Indoles/metabolism , Models, Chemical , Epoxy Compounds/chemistry , Epoxy Compounds/metabolism , Flavin-Adenine Dinucleotide/chemistry , Flavin-Adenine Dinucleotide/metabolism , Models, MolecularABSTRACT
Flavoenzymes catalyze numerous redox reactions including the transfer of an O2-derived oxygen atom to organic substrates, while the other one is reduced to water. Investigation of some of these monooxygenases led to a detailed understanding of their catalytic cycle, which involves the flavin-C4α-(hydro)peroxide as hallmark oxygenating species, and newly discovered flavoprotein monooxygenases were generally assumed to operate similarly. However, discoveries in recent years revealed a broader mechanistic versatility, including enzymes that utilize flavin-N5 oxygen adducts for catalysis in the form of the flavin-N5-(hydro)peroxide and the flavin-N5-oxide species. In this review, I will highlight recent developments in that area, including noncanonical flavoenzymes from natural product biosynthesis and sulfur metabolism that provide first insights into the chemical properties of these species. Remarkably, some enzymes may even combine the flavin-N5-peroxide and the flavin-N5-oxide species for consecutive oxygen-transfers to the same substrate and thereby in essence operate as dioxygenases.
Subject(s)
Flavins , Oxidation-Reduction , Oxygen , Oxygen/metabolism , Oxygen/chemistry , Flavins/metabolism , Flavins/chemistry , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Flavoproteins/metabolism , Flavoproteins/chemistryABSTRACT
OxaD is a flavin-dependent monooxygenase (FMO) responsible for catalyzing the oxidation of an indole nitrogen atom, resulting in the formation of a nitrone. Nitrones serve as versatile intermediates in complex syntheses, including challenging reactions like cycloadditions. Traditional organic synthesis methods often yield limited results and involve environmentally harmful chemicals. Therefore, the enzymatic synthesis of nitrone-containing compounds holds promise for more sustainable industrial processes. In this study, we explored the catalytic mechanism of OxaD using a combination of steady-state and rapid-reaction kinetics, site-directed mutagenesis, spectroscopy, and structural modeling. Our investigations showed that OxaD catalyzes two oxidations of the indole nitrogen of roquefortine C, ultimately yielding roquefortine L. The reductive-half reaction analysis indicated that OxaD rapidly undergoes reduction and follows a "cautious" flavin reduction mechanism by requiring substrate binding before reduction can take place. This characteristic places OxaD in class A of the FMO family, a classification supported by a structural model featuring a single Rossmann nucleotide binding domain and a glutathione reductase fold. Furthermore, our spectroscopic analysis unveiled both enzyme-substrate and enzyme-intermediate complexes. Our analysis of the oxidative-half reaction suggests that the flavin dehydration step is the slow step in the catalytic cycle. Finally, through mutagenesis of the conserved D63 residue, we demonstrated its role in flavin motion and product oxygenation. Based on our findings, we propose a catalytic mechanism for OxaD and provide insights into the active site architecture within class A FMOs.
Subject(s)
Mixed Function Oxygenases , Nitrogen Oxides , Oxidation-Reduction , Nitrogen Oxides/metabolism , Nitrogen Oxides/chemistry , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Mixed Function Oxygenases/genetics , Kinetics , Mutagenesis, Site-Directed , Flavins/metabolism , Flavins/chemistry , Models, Molecular , Bacterial Proteins/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , OxygenasesABSTRACT
Oxidoreductases have evolved tyrosine/tryptophan pathways that channel highly oxidizing holes away from the active site to avoid damage. Here we dissect such a pathway in a bacterial LPMO, member of a widespread family of C-H bond activating enzymes with outstanding industrial potential. We show that a strictly conserved tryptophan is critical for radical formation and hole transference and that holes traverse the protein to reach a tyrosine-histidine pair in the protein's surface. Real-time monitoring of radical formation reveals a clear correlation between the efficiency of hole transference and enzyme performance under oxidative stress. Residues involved in this pathway vary considerably between natural LPMOs, which could reflect adaptation to different ecological niches. Importantly, we show that enzyme activity is increased in a variant with slower radical transference, providing experimental evidence for a previously postulated trade-off between activity and redox robustness.
Subject(s)
Bacterial Proteins , Mixed Function Oxygenases , Oxidation-Reduction , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/genetics , Mixed Function Oxygenases/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Catalytic Domain , Tryptophan/metabolism , Polysaccharides/metabolism , Mutation , Oxidative Stress , Tyrosine/metabolism , Models, Molecular , Histidine/metabolism , Histidine/geneticsABSTRACT
CYP116B5 is a class VII P450 in which the heme domain is linked to a FMN and 2Fe2S-binding reductase. Our laboratory has proved that the CYP116B5 heme domain (CYP116B5-hd) is capable of catalyzing the oxidation of substrates using H2O2. Recently, the Molecular Lego approach was applied to join the heme domain of CYP116B5 to sarcosine oxidase (SOX), which provides H2O2 in-situ by the sarcosine oxidation. In this work, the chimeric self-sufficient fusion enzyme CYP116B5-SOX was heterologously expressed, purified, and characterized for its functionality by absorbance and fluorescence spectroscopy. Differential scanning calorimetry (DSC) experiments revealed a TM of 48.4 ± 0.04 and 58.3 ± 0.02°C and a enthalpy value of 175,500 ± 1850 and 120,500 ± 1350 cal mol-1 for the CYP116B5 and SOX domains respectively. The fusion enzyme showed an outstanding chemical stability in presence of up to 200 mM sarcosine or 5 mM H2O2 (4.4 ± 0.8 and 11.0 ± 2.6% heme leakage respectively). Thanks to the in-situ H2O2 generation, an improved kcat/KM for the p-nitrophenol conversion was observed (kcat of 20.1 ± 0.6 min-1 and KM of 0.23 ± 0.03 mM), corresponding to 4 times the kcat/KM of the CYP116B5-hd. The aim of this work is the development of an engineered biocatalyst to be exploited in bioremediation. In order to tackle this challenge, an E. coli strain expressing CYP116B5-SOX was employed to exploit this biocatalyst for the oxidation of the wastewater contaminating-drug tamoxifen. Data show a 12-fold increase in tamoxifen N-oxide production-herein detected for the first time as CYP116B5 metabolite-compared to the direct H2O2 supply, equal to the 25% of the total drug conversion.